big changes to shell lesson

lessons/2-shell/notes.qmd

@@ -24,33 +24,38 @@ format: html
     -   Split into 2 breakout rooms to install on different OS's.
 -   Break to all download shell-lesson-data
     -   Link
-    -   Put it somewhere high in the file system (Desktop)
-    -   Unzip using command line unzip (or just point-and-click in computer file system?)
--   Live coding: Intro to the terminal pane in RStudio
-    -   Quick tour of RStudio panes
-        -   Emphasize files pane, analogous to Finder/File Explorer
-        -   Navigate to shell-lesson-data
-    -   Everyone set up to use bash with Terminal pane
-    -   Show navigation to Current Directory in Terminal pane in RStudio
-        -   Make sure everyone ends up in shell-lesson-data
--   Live coding: Unix Shell lesson 1
-    -   https://swcarpentry.github.io/shell-novice/01-intro
-    -   (a lot of the text the content of this lesson will be covered in the slides section above)
+    -   Put it on your Desktop
+    -   Unzip using point-and-click
+-   Live coding: Setup RStudio
+    -   Open RStudio
+    -   Tour panes: files and  terminal
+    -   Set up terminal pane to use bash
+-   Live coding: Navigating filesystems in files pane
+    -   Use file pane to navigate to shell-lesson-data
+-   Live coding: Navigate to shell-lesson-data in Terminal 
     -   Identify the prompt and note that it is different in zsh (%)
-    -   Introduce ls
-    -   Introduce `command not found`
-    -   Introduce general anatomy of a shell prompt (Slide/share image)
--   Live coding: Unix Shell lesson 2
-    -   `pwd` and file systems
-    -   Using options and getting help
-    -   Navigating around file systems
--   (Time-permitting) live coding: Unix Shell lesson 3
-    -   Creating directories
-    -   Creating and editing text files
-    -   Moving and renaming files and directories
-    -   Copying
-    -   Removing
-    -   Wildcards
+    - `pwd`
+    - `cd`
+    - `ls`
+        - Use `ls` flags to explain anatomy of a shell command
+        - Show `man ls` to show flag options for the `ls` command
+-   Live coding: Synchronizing file panes
+    - Show "Go to current directory" to bring Terminal to files pane
+    - Show "New terminal here" to create a terminal in files pane
+    - Show that Rstudio's working directory is not automatically wherever either Terminal or the file pane is
+- Live coding: using Rprojects to simplify filesystems
+    - Create an R project
+    - Show that, upon opening, Terminal, getwd(), and file pane are all on the same page
+- Live coding: `cp` and `move`
+    - Copy `shell_lesson_data` to the Rproject.
+    - Tell them we need `cp`, then use `man cp` to get the options
+    - Repeat using `ls` to explore contents of `shell_lesson_data` and mirror files pane
+-   Live coding/discussion: options for finding help
+    - `--help` flag
+    - `man` pages
+    - Manual pages: `?` in R, package websites
+    - StackOverflow
+    - ChatGPT
 -   Homework for next session
     -   Read <https://peerj.com/preprints/3159/> git (Version control prep)
     -   Create a diagram of your file system and note your most frequently used directories

lessons/2-shell/slides.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Shell Commands"
+title: "Shell and Filesystems"
 subtitle: "Session 2"
 # date: TODO
 format: revealjs
@@ -16,10 +16,9 @@ footer: "[Reproduciblity & Data Science in R](../../index.html)"
 # Learning objectives
 
 -   Understand the what and why of the shell
--   Interact with the shell using common commands
--   Find help via --help, man, and online help pages
--   Navigate your file system from the command line
--   (Time permitting) Manipulate and move files from the command line
+-   Use the shell to navigate your computer's file system
+-   Use R projects to simplify file system navigation
+-   Know your options for finding help
 
 # What is the shell?
 
@@ -31,13 +30,21 @@ footer: "[Reproduciblity & Data Science in R](../../index.html)"
 -   Batch large tasks (e.g. renaming files)
 -   Interact with remote computers like the University HPC
 
+# Shell in this workshop
+
+-   git/GitHub (next 2 lessons)
+-   Navigating your file system
+-   Quarto (lesson 9)
+
 # Let's get set up!
 
 -   macOS comes with a shell (usually Bash or Zsh) built-in
 
 -   Windows need to install GitBash (includes Bash shell and git, which we will use later)
 
 -   Breakout rooms
+    - Mac users go with Eric
+    - Windows users go with Renata
 
 # Data download
 
@@ -47,25 +54,106 @@ footer: "[Reproduciblity & Data Science in R](../../index.html)"
 
 # Coding time
 
--   Intro to shell commands
+- RStudio panes
+- Set up Terminal in RStudio
+- Navigation using Terminal and Files pane
+
+# Example file system
+
+![](file-path-example.png)
+
+# Example file system
+
+![](file-structure-example.png)
 
 # Syntax of a shell command
 
 ![](shell_syntax.png){fig-align="center"}
 
 # Coding time
 
--   File systems
+- Synchronize working directories between Terminal, Files Pane, and R working directory
 
-# Example file system
+# Coding time
 
-![](file-path-example.png)
+- Use an R project to simplify working directories
+- Copy `shell_lesson_data` to your R project 
+
+# Getting help
+
+```bash
+man ls
+```
+
+# Getting help
+
+```bash
+git --help
+```
+
+# Getting help
+
+![](getwd.png){fig-align="center"}
+
+# Getting help
+
+![](man_page.png){fig-align="center"}
+
+
+# Getting help
+
+![](stack_overflow.png){fig-align="center"}
+
+# Getting help
+
+![](gpt.png){fig-align="center"}
+
+# Beware of stochastic parrots
+
+-   LLMs don't _understand_, but are good at mimicry
+-   Use with care:
+    -   May be wrong
+    -   May be inconsistent
+
+# Beware of stochastic parrots
+
+-   Tools like ChatGPT pose ethical issues
+    -   Plagiarism
+    -   Labor conditions
+    -   Inputs may be sent to parent companies
+
+# Getting help: fellow humans
+
+![](ua-ds-slack.png){fig-align="center"}
+
+
+# Getting help: fellow humans
+
+![](drop-ins.png){fig-align="center"}
 
-# Example file system
 
-![](file-structure-example.png)
 
 # Homework for next time
 
 -   Read ["Excuse me, do you have a moment to talk about version control?"](https://peerj.com/preprints/3159/)
 -   Create a diagram of your file system and note your most frequently used directories
+
+# Resources: Shell
+
+-   [Software Carpentry Unix Shell episode #1](https://swcarpentry.github.io/shell-novice/01-intro)
+-  [Software Carpentry Unix Shell episode #2](https://swcarpentry.github.io/shell-novice/02-filedir)
+-  [Software Carpentry Unix Shell episode #3](https://swcarpentry.github.io/shell-novice/03-create)
+
+# Resources: AI tools
+
+-   <https://ecoevo.social/@cboettig/110934209180569370>
+-   <https://www.infoworld.com/article/3694611/8-chatgpt-tools-for-r-programming.html>
+-   <https://en.wikipedia.org/wiki/Stochastic_parrot>
+-   <https://dl.acm.org/doi/abs/10.1145/3442188.3445922>
+-   <https://medium.com/@konstantine_45825/chatgpt-is-no-stochastic-parrot-but-it-also-claims-that-1-is-greater-than-1-e3cd1fc303e0>
+
+# Resources: UA community
+
+- [UA Data Science Institute](https://datascience.arizona.edu/)
+- [UA Data Science Slack](https://jcoliver.github.io/uadatascience-slack/)
+- [CCT Drop-in Hours, 9-10 on Tuesdays](https://datascience.cct.arizona.edu/drop-in-hours)